Suspended matter samples filtered from surface waters and two depth profiles from the Flores Sea and Makasar Strait were investigated by electron probe X-ray microanalysis (EPXMA) and laser microprobe mass analysis (LAMMA). EPXMA yielded discrete morphological and chemical analysis of the major particle types of suspended matter. Cluster analysis revealed that thirteen main particle types described the composition of suspended matter of the Flores Sea and Makasar Strait. Silicates, aluminosilicates and Fe-oxyhydroxides were the predominant particle types. Suspended matter of the basins studied contained high levels of tin-bearing particles. On the basis of their composition, tin particles can be divided into three groups: (1) tin oxide/hydroxides (cassiterite, romarchite, hydroromarchite); (2) iron-oxyhydroxides with adsorbed tin; and (3) mixed oxidation state tin hydroxysulphates. Only ultra-fine cassiterite particles enter the seawater in suspended state. Dissolved tin species entering the sea have three alternatives: (1) to be scavenged by Fe-oxyhydroxides; (2) to precipitate as tin oxide/hydroxides (romarchite, hydroromarchite); (3) to precipitate as tin hydroxysulphates. The conclusion is that dissolved and suspended tin originate from local sources in the land frame of the basins as well as from remote sources in the Indonesian Archipelago. Four different sectors of the waters studied have suspended matter with different composition: (1) the Mahakam River--Delta zone; (2) the open Flores Sea; (3) the landlocked Saleh Bay; (4) the Makasar Strait proper. The depth distribution of suspended particle types is mainly influenced by: (1) the bottom nepheloid layer and calcite lysocline in the Flores Sea; (2) the high bioproduction in the surface water layer and the vertical distribution of organic matter in the Makasar Strait.